Analysis of circulating cell-free DNA (cfDNA) using next generation sequencing (NGS) is recognized as a valuable tool for detection and diagnosis of cancer. Current protocols for preparing cfDNA for sequencing typically include ligation of double-stranded DNA (dsDNA) to sequencing adapters. However, a cfDNA sample typically includes other populations of DNA, such as single-stranded DNA (ssDNA) and/or damaged DNA (e.g., nicked DNA) that are not captured in a double-stranded ligation reaction. Because only the dsDNA population is captured during library preparation, precious cell-free nucleic acid material (e.g., ssDNA and/or damaged DNA) is wasted and valuable diagnostic information may be lost. There is a need for new methods of preparing a sequencing library from a cfDNA sample that captures ssDNA, dsDNA, and damaged DNA populations for sequence analysis.